Contact

 pcherry [at] pm dot me |  upon request |  Senior Scientist | Genomics |  Twist Bioscience |  San Francisco, California |  pdcherry.github.io |  github.com/pdcherry |  linkedin.com/in/p-cherry |  United States Citizen |

Last updated on 2024-12-10.

Data-driven résumé made in R using pagedown.

Main

Patrick Cherry

PhD scientist skilled in RNA biochemistry, next-generation sequencing (NGS), bioinformatics, biological data science, data visualization, and tool-building. I’ve invented highly multiplexed RNA and DNA methods, coded reproducible and rigorous pipelines for high-throughput experimental designs and genomic analyses, and launched best-in-class oncology reference standards. Originally trained in Molecular Biology, I’m interested in taking my knowledge and practice of RNA biology and bioinformatics to the next level.

Education

PhD

University of Colorado School of Medicine

Aurora/Denver, Colorado

May 2019 - Aug 2013

  • Ph.D. in Molecular Biology. Advisor: Jay Hesselberth, PhD
  • Thesis: RNA terminus chemistry impact decay events that target HAC1 mRNA during the Unfolded Protein Response

BA

Hendrix College

Conway, Arkansas

May 2013 - Aug 2009

  • Biochemistry and Molecular Biology, with Distinction. Advisor: Andres Caro, PhD
  • Senior Capstone Project showing key stress response gene expression changes to oxidative stress in liver cells
  • Minor in Mathematics; PI: Lars Seme; Project: Newton’s method as a fractal chaotic dynamical system

Industry Experience

I currently split my time between wet lab and computational activities. I have worked in a variety of roles ranging from HTP strain onboarding to genomics scientist. I like collaborative environments where I can learn from my peers and in turn teach others.

Senior Scientist, Oncology

BillionToOne

Menlo Park, CA

Current - Sep 2024

  • Devised and validated precise high-throughput DNA quantification process for accurate pooling; on-boarded droplet digital PCR (ddPCR) system into production; designed and validated custom ddPCR assays for use in production
  • Generated 500+ automated ddPCR primer / probe designs with pipeline in snakemake using s3 database of variant data and primer3 primer selection

Senior Scientist, Genomics

Twist Bioscience

South San Francisco, California

Apr 2024 - Jan 2021

  • Invented and introduced multiple new products to market, yielding $1M+ in new revenue as Tech Lead, including: Pan-cancer cfDNA (v1 & v2), CNV Controls, RNA Fusion Controls, Fragmentome Controls, RNA-seq, and primer / adapter removal methods for highly-multiplexed dsDNA pools
  • Built positive team culture; mentored and promoted a report from Senior Research Associate to Scientist; Coached reports who served as Tech Leads; Delivered quality science on deadline by managing research assistants; Guided cross-functional teams through product launch and beyond
  • Original research and presentations to non-experts and outside stakeholders unveiled novel products and underwrote multiple patents; Gained new customers in RNA standards space with the design and launch of HTP RNA synthesis
  • Analyzed public databases and feedback from alpha testers to optimize design of multiple products; routinely crafted custom data analysis pipelines in R and Python; documented analyses using Rmarkdown, Quarto, and Jupyter; maintained git repo of dockerized bioinformatic QC packages for Pan-cancer cfDNA standards line
  • Generated actionable data for new technology evaluations of a new NGS platform with custom experiments and bioinformatic analyses in Python, R, and SQL to enable faster gene QC in Production; launched a time-saving gene synthesis change into production, supported by original experimental data; boosted colleagues in publication-ready plots by coding and distributing on company GitHub the internal package twistcolorpal; Regularly use R, Python, and AWS, locally and on Databricks; regularly implements and runs automated code tests
  • Led multiple iterations of custom NGS analysis; refined the QC approach and thresholds for ensuring a contamination-free production process; extensively used data visualization to communicate complex data to cross-functional teams; extensively used UMI sequencing and created novel method to rigorously quantify library conversion efficiency to evaluate products and reference materials

Scientist I, NGS & Strain-Build Process Development

Zymergen, Inc.

Emeryville, California

Jan 2021 - Apr 2019

  • Achieved a 95% success rate for obtaining genetic edits by designing and implementing multiple automated high-throughput methods for a non-model microbe: transformation, counterselection, and NGS genotyping
  • Boosted NGS Core genotyping success by 45% using data-driven decision-making and teaching; Guided demanding and diverse internal customers on complex NGS experiments and data interpretation
  • Determined best methods for genetic manipulation, propagation, and archiving of a non-model microbe through design & execution of complex experiments (DoE) on lab automation, with and without LIMS sample tracking
  • Delivered robust process while working on New Product Introduction team; applied statistical methods to screen and optimize a genetic engineering process for newly-on-boarded non-model microbe.
  • Delivered on KPIs for microbe improvement by designing and building hundreds of plasmids using modern molecular techniques like Gibson, Golden Gate, and yeast assembly

Research Experience

I worked on a few projects during my PhD, and the RNA repair project led me to custom 5′-OH RNA-seq libraries, which inspired my fascination with transcriptomics and bioinformatics.

Doctoral Research

University of Colorado School of Medicine

Aurora/Denver, Colorado

May 2019 - May 2014

  • Wrote, revised, & published two academic papers on RNA repair & yeast genetics
  • Engineered and characterized genetic bypass of essential genes in budding yeast; on-boarded CRISPR/Cas9 for efficient and precise gene knock-in and scarless knock-out
  • Cultured large batches of wild-type and mutant E. coli to expressed and purified recombinant proteins, which enabled carrying out RNA library prep and RNA modification enzymatic assays
  • Optimized custom RNA-seq library protocol; independently planned, executed, troubleshooted RNA modification detection
  • Routinely conducted northern blotting, targeted depletion, primer extension, splinted ligation, and other esoteric DNA and RNA experiments

Intellectual Property

Working at Twist and Zymergen on new product research requires confidentiality, but public evidence of accomplishments often comes in patent applications. The Legal teams know me well for being a helpful expert in the process.

Libraries for mutational analysis

Twist Bioscience

South San Francisco, California

Apr 2021

  • US Prov. Pat. Ref No 823.101
  • Configuration and fabrication of synthetic DNA & RNA reference standards and synthetic variant sequences

Method for counterselection in microorganisms

Zymergen, Inc.

Emeryville, California

Mar 2021

  • US 2021_0087586 A1
  • Demonstration of novel counterselection mechanism in non-model Bacillus microbe for genetic modification

Selected Publications

I communicate my results clearly, both in writing and in live presentations. I enjoy writing research papers, but my career has required more tech notes and app notes recently.

Twist cfDNA Pan-Cancer Reference Standard v2 Technical Guidance

Twist Bioscience Product Sheet & FAQ

South San Francisco, California

Jan 2024

  • Patrick Cherry, Lydia Bonar, & Mike Bocek

Characteristics and specificity of the wild-type / 0% VAF reference material

Twist Bioscience

South San Francisco, California

Apr 2022

  • Patrick Cherry & Mike Bocek

Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response

eLife

Aurora/Denver, Colorado

Mar 2019

  • Cherry, P., Peach, S., & Hesselberth, J.

Genetic bypass of essential RNA repair enzymes in budding yeast

RNA

Aurora/Denver, Colorado

Dec 2017

  • Cherry, P., White, L., York, K., & Hesselberth, J.

Selected Presentations & Talks

I give audience-centered presentations by adapting on the fly and over time to the venue and occasion. I like to transfer knowledge by giving methods/best practices talks whose slides can also serve as documentation.

Twist pan-cancer reference standard V2: Enhanced precision and reduced errors in ctDNA analysis

Advances in Genome Biology and Technology, Twist Bioscience

Orlando, Florida

Feb 2024

Twist pan-cancer synthetic RNA fusion control for assay development

American Association for Cancer Researchers, Twist Bioscience

Orlando, Florida

Apr 2023

Use of synthetic CNV fragments to mimic copy number alterations for ctDNA reference standards

Advances in Genome Biology and Technology, Twist Bioscience

Hollywood, Florida

Feb 2023

Twist pan-cancer synthetic reference materials for cell-free DNA (cfDNA) assay development

American Association for Cancer Researchers, Twist Bioscience

New Orleans, Louisiana

Apr 2022

R use at Zymergen

Z-Tech Talk

Emeryville, CA

Jun 2020

Data-driven troubleshooting of NGS experiments

Data Science Talk

Emeryville, CA

Apr 2020

RNA processing regulates the unfolded protein response

CSHL: mRNA Processing Meeting Talk

Cold Spring Harbor, New York

Aug 2017